From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Jun 07 2012 - 10:40:35 CDT
Your input looks fine, no problems there. As mentioned, the issue is
probably either the input PSF/COOR or the machine. I suspect the issue
might be memory. How much mem is present on the box you are using to
compress the psf? Can you retry on a box with larger available mem?
On Thu, Jun 7, 2012 at 8:11 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> I just successfully tried your configuration file but with a different PSF
> file, coordinate file, and parameter files (obviously), and it worked fine
> with the standard NAMD 2.9 build (NOT memopt) on one processor. I'm not
> sure what else to suggest, except trying it A) with different input files
> and B) on a different computer.
> Info: TIME FOR READING PSF FILE: 36.7447
> Bond sigs: 264
> Angle sigs: 861
> Dihedral sigs: 1499
> Improper sigs: 74
> Crossterm sigs: 45
> Atom's sigs: 1656
> Exclusion signatures: 2210
> Finished compressing molecule information, which takes 23.8148(s)
> Program finished.
> On Jun 7, 2012, at 7:02 AM, Cruz-Chu Eduardo Roberto wrote:
> > Hi;
> > I am still trying to generate the INTER file. That is, just the first
> step before running anything, only switching the structure file using
> "genCompressedPsf on".
> > Not need of "useCompressedPsf on" yet, just the INTER file.
> > So I moved to a small system of about 9000 atoms, just to check the
> thing is working. Unfortunately, I was not able to obtain the INTER file--e89a8f3ba11567b2c304c1e3b4cc--
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